AMR++ Bioinformatic pipeline

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.15

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        AMR++ Bioinformatic pipeline
        A pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Contact E-mail
        meglab.metagenomics@gmail.com
        Application Type
        AMR++
        Project Type
        FastQC analysis

        Report generated on 2024-01-31, 22:35 CST based on data in:

        General Statistics

        Showing 328/328 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        1-2GRA-1-1-Fec-TE_S13_L001_R1_001
        71.5%
        51%
        17.0
        1-2GRA-1-1-Fec-TE_S13_L001_R2_001
        70.6%
        51%
        17.0
        1-2GRA-1-3-Fec-TE_S85_L001_R1_001
        70.2%
        50%
        16.0
        1-2GRA-1-3-Fec-TE_S85_L001_R2_001
        69.3%
        50%
        16.0
        1-2GRA-1-4-Fec-TE_S62_L001_R1_001
        66.5%
        52%
        18.5
        1-2GRA-1-4-Fec-TE_S62_L001_R2_001
        65.5%
        52%
        18.5
        1-2GRA-1-5-Fec-TE_S133_L001_R1_001
        79.3%
        51%
        24.3
        1-2GRA-1-5-Fec-TE_S133_L001_R2_001
        77.8%
        51%
        24.3
        1-2GRA-1-6-Fec-TE_S47_L001_R1_001
        69.7%
        50%
        16.5
        1-2GRA-1-6-Fec-TE_S47_L001_R2_001
        69.2%
        51%
        16.5
        1-2GRA-1-7-Fec-TE_S59_L001_R1_001
        75.8%
        51%
        21.1
        1-2GRA-1-7-Fec-TE_S59_L001_R2_001
        74.6%
        51%
        21.1
        1-2GRA-1-8-Fec-TE_S57_L001_R1_001
        76.4%
        50%
        20.8
        1-2GRA-1-8-Fec-TE_S57_L001_R2_001
        75.2%
        50%
        20.8
        1-2GRA-2-1-Fec-TE_S34_L001_R1_001
        77.9%
        51%
        19.9
        1-2GRA-2-1-Fec-TE_S34_L001_R2_001
        76.9%
        51%
        19.9
        1-2GRA-2-2-Fec-TE_S107_L001_R1_001
        69.8%
        50%
        20.5
        1-2GRA-2-2-Fec-TE_S107_L001_R2_001
        68.7%
        51%
        20.5
        1-2GRA-2-3-Fec-TE_S53_L001_R1_001
        70.2%
        50%
        16.5
        1-2GRA-2-3-Fec-TE_S53_L001_R2_001
        69.5%
        51%
        16.5
        1-2GRA-2-4-Fec-TE_S152_L001_R1_001
        72.3%
        50%
        18.1
        1-2GRA-2-4-Fec-TE_S152_L001_R2_001
        71.8%
        50%
        18.1
        1-2GRA-2-4Vag-TE_S162_L001_R1_001
        96.3%
        49%
        19.5
        1-2GRA-2-4Vag-TE_S162_L001_R2_001
        95.2%
        49%
        19.5
        1-2GRA-2-5-Fec-TE_S5_L001_R1_001
        76.3%
        51%
        21.4
        1-2GRA-2-5-Fec-TE_S5_L001_R2_001
        75.3%
        51%
        21.4
        1-2GRA-2-5Nas-TE_S160_L001_R1_001
        96.0%
        52%
        26.6
        1-2GRA-2-5Nas-TE_S160_L001_R2_001
        94.5%
        52%
        26.6
        1-2GRA-2-6-Fec-TE_S156_L001_R1_001
        14.9%
        48%
        27.9
        1-2GRA-2-6-Fec-TE_S156_L001_R2_001
        15.1%
        49%
        27.9
        1-2GRA-2-7-Fec-TE_S95_L001_R1_001
        73.7%
        50%
        20.0
        1-2GRA-2-7-Fec-TE_S95_L001_R2_001
        73.3%
        50%
        20.0
        1-2GRA-2-8-Fec-TE_S73_L001_R1_001
        79.0%
        50%
        25.5
        1-2GRA-2-8-Fec-TE_S73_L001_R2_001
        78.1%
        50%
        25.5
        1-2GRA-3-1-Fec-TE_S138_L001_R1_001
        74.1%
        50%
        21.2
        1-2GRA-3-1-Fec-TE_S138_L001_R2_001
        72.8%
        50%
        21.2
        1-2GRA-3-2-Fec-TE_S125_L001_R1_001
        72.8%
        51%
        21.1
        1-2GRA-3-2-Fec-TE_S125_L001_R2_001
        71.6%
        51%
        21.1
        1-2GRA-3-3-Fec-TE_S3_L001_R1_001
        73.0%
        51%
        18.8
        1-2GRA-3-3-Fec-TE_S3_L001_R2_001
        71.7%
        51%
        18.8
        1-2GRA-3-4-Fec-TE_S1_L001_R1_001
        69.9%
        51%
        20.1
        1-2GRA-3-4-Fec-TE_S1_L001_R2_001
        67.8%
        51%
        20.1
        1-2GRA-3-5-Fec-TE_S54_L001_R1_001
        70.2%
        51%
        19.3
        1-2GRA-3-5-Fec-TE_S54_L001_R2_001
        70.0%
        51%
        19.3
        1-2GRA-3-6-Fec-TE_S147_L001_R1_001
        70.9%
        51%
        19.7
        1-2GRA-3-6-Fec-TE_S147_L001_R2_001
        70.5%
        51%
        19.7
        1-2GRA-3-7-Fec-TE_S84_L001_R1_001
        69.4%
        50%
        16.9
        1-2GRA-3-7-Fec-TE_S84_L001_R2_001
        69.0%
        51%
        16.9
        1-2GRA-3-8-Fec-TE_S58_L001_R1_001
        71.1%
        49%
        15.8
        1-2GRA-3-8-Fec-TE_S58_L001_R2_001
        70.4%
        49%
        15.8
        1-2GRA-4-1-Fec-TE_S15_L001_R1_001
        68.7%
        51%
        13.6
        1-2GRA-4-1-Fec-TE_S15_L001_R2_001
        67.0%
        51%
        13.6
        1-2GRA-4-2-Fec-TE_S116_L001_R1_001
        66.7%
        51%
        19.8
        1-2GRA-4-2-Fec-TE_S116_L001_R2_001
        65.5%
        51%
        19.8
        1-2GRA-4-3-Fec-TE_S72_L001_R1_001
        71.4%
        50%
        17.1
        1-2GRA-4-3-Fec-TE_S72_L001_R2_001
        70.7%
        51%
        17.1
        1-2GRA-4-4-Fec-TE_S101_L001_R1_001
        75.4%
        51%
        16.9
        1-2GRA-4-4-Fec-TE_S101_L001_R2_001
        74.4%
        51%
        16.9
        1-2GRA-4-5-Fec-TE_S10_L001_R1_001
        72.9%
        49%
        17.4
        1-2GRA-4-5-Fec-TE_S10_L001_R2_001
        72.3%
        49%
        17.4
        1-2GRA-4-5Vag-TE_S164_L001_R1_001
        96.5%
        52%
        21.3
        1-2GRA-4-5Vag-TE_S164_L001_R2_001
        95.7%
        52%
        21.3
        1-2GRA-4-6-Fec-TE_S71_L001_R1_001
        75.7%
        52%
        20.7
        1-2GRA-4-6-Fec-TE_S71_L001_R2_001
        75.4%
        52%
        20.7
        1-2GRA-4-7-Fec-TE_S92_L001_R1_001
        63.1%
        50%
        21.3
        1-2GRA-4-7-Fec-TE_S92_L001_R2_001
        62.6%
        50%
        21.3
        1-2GRA-4-8-Fec-TE_S63_L001_R1_001
        81.6%
        51%
        20.6
        1-2GRA-4-8-Fec-TE_S63_L001_R2_001
        81.0%
        51%
        20.6
        1-2GRA-5-1-Fec-TE_S18_L001_R1_001
        73.4%
        51%
        17.1
        1-2GRA-5-1-Fec-TE_S18_L001_R2_001
        72.7%
        51%
        17.1
        1-2GRA-5-2-Fec-TE_S66_L001_R1_001
        73.6%
        50%
        15.9
        1-2GRA-5-2-Fec-TE_S66_L001_R2_001
        73.1%
        50%
        15.9
        1-2GRA-5-3-Fec-TE_S117_L001_R1_001
        71.8%
        51%
        22.9
        1-2GRA-5-3-Fec-TE_S117_L001_R2_001
        71.3%
        51%
        22.9
        1-2GRA-5-4-Fec-TE_S145_L001_R1_001
        70.0%
        51%
        17.4
        1-2GRA-5-4-Fec-TE_S145_L001_R2_001
        69.3%
        51%
        17.4
        1-2GRA-5-5-Fec-TE_S146_L001_R1_001
        68.7%
        52%
        17.1
        1-2GRA-5-5-Fec-TE_S146_L001_R2_001
        68.1%
        52%
        17.1
        1-2GRA-5-6-Fec-TE_S32_L001_R1_001
        71.6%
        52%
        17.0
        1-2GRA-5-6-Fec-TE_S32_L001_R2_001
        70.8%
        52%
        17.0
        1-2GRA-5-7-Fec-TE_S88_L001_R1_001
        72.0%
        52%
        20.8
        1-2GRA-5-7-Fec-TE_S88_L001_R2_001
        71.5%
        52%
        20.8
        1-2GRA-5-8-Fec-TE_S49_L001_R1_001
        71.3%
        51%
        18.3
        1-2GRA-5-8-Fec-TE_S49_L001_R2_001
        70.7%
        51%
        18.3
        3-4GRA-1-1-Fec-TE_S149_L001_R1_001
        72.3%
        50%
        14.4
        3-4GRA-1-1-Fec-TE_S149_L001_R2_001
        71.8%
        50%
        14.4
        3-4GRA-1-3-Fec-TE_S87_L001_R1_001
        73.4%
        50%
        14.3
        3-4GRA-1-3-Fec-TE_S87_L001_R2_001
        72.5%
        50%
        14.3
        3-4GRA-1-4-Fec-TE_S65_L001_R1_001
        77.2%
        51%
        20.4
        3-4GRA-1-4-Fec-TE_S65_L001_R2_001
        76.2%
        51%
        20.4
        3-4GRA-1-5-Fec-TE_S23_L001_R1_001
        75.4%
        50%
        16.8
        3-4GRA-1-5-Fec-TE_S23_L001_R2_001
        74.6%
        50%
        16.8
        3-4GRA-1-6-Fec-TE_S122_L001_R1_001
        74.9%
        50%
        19.3
        3-4GRA-1-6-Fec-TE_S122_L001_R2_001
        74.1%
        50%
        19.3
        3-4GRA-1-7-Fec-TE_S140_L001_R1_001
        72.3%
        50%
        21.6
        3-4GRA-1-7-Fec-TE_S140_L001_R2_001
        71.8%
        50%
        21.6
        3-4GRA-1-8-Fec-TE_S113_L001_R1_001
        65.1%
        50%
        15.3
        3-4GRA-1-8-Fec-TE_S113_L001_R2_001
        63.7%
        50%
        15.3
        3-4GRA-2-1-Fec-TE_S50_L001_R1_001
        82.5%
        51%
        17.7
        3-4GRA-2-1-Fec-TE_S50_L001_R2_001
        81.6%
        51%
        17.7
        3-4GRA-2-2-Fec-TE_S150_L001_R1_001
        71.6%
        50%
        15.6
        3-4GRA-2-2-Fec-TE_S150_L001_R2_001
        71.3%
        50%
        15.6
        3-4GRA-2-3-Fec-TE_S69_L001_R1_001
        75.4%
        50%
        17.1
        3-4GRA-2-3-Fec-TE_S69_L001_R2_001
        74.5%
        50%
        17.1
        3-4GRA-2-4-Fec-TE_S31_L001_R1_001
        78.0%
        50%
        21.7
        3-4GRA-2-4-Fec-TE_S31_L001_R2_001
        77.6%
        50%
        21.7
        3-4GRA-2-5-Fec-TE_S33_L001_R1_001
        67.7%
        51%
        14.3
        3-4GRA-2-5-Fec-TE_S33_L001_R2_001
        66.5%
        51%
        14.3
        3-4GRA-2-6-Fec-TE_S89_L001_R1_001
        71.9%
        51%
        19.4
        3-4GRA-2-6-Fec-TE_S89_L001_R2_001
        71.4%
        52%
        19.4
        3-4GRA-2-7-Fec-TE_S16_L001_R1_001
        73.6%
        51%
        17.9
        3-4GRA-2-7-Fec-TE_S16_L001_R2_001
        72.9%
        51%
        17.9
        3-4GRA-2-8-Fec-TE_S27_L001_R1_001
        75.2%
        50%
        18.5
        3-4GRA-2-8-Fec-TE_S27_L001_R2_001
        74.8%
        50%
        18.5
        3-4GRA-3-1-Fec-TE_S129_L001_R1_001
        72.5%
        47%
        18.6
        3-4GRA-3-1-Fec-TE_S129_L001_R2_001
        72.5%
        47%
        18.6
        3-4GRA-3-2-Fec-TE_S98_L001_R1_001
        74.1%
        48%
        20.9
        3-4GRA-3-2-Fec-TE_S98_L001_R2_001
        73.6%
        48%
        20.9
        3-4GRA-3-3-Fec-TE_S105_L001_R1_001
        70.5%
        47%
        20.2
        3-4GRA-3-3-Fec-TE_S105_L001_R2_001
        69.4%
        47%
        20.2
        3-4GRA-3-4-Fec-TE_S8_L001_R1_001
        68.8%
        48%
        20.1
        3-4GRA-3-4-Fec-TE_S8_L001_R2_001
        67.6%
        48%
        20.1
        3-4GRA-3-5-Fec-TE_S29_L001_R1_001
        72.8%
        47%
        18.4
        3-4GRA-3-5-Fec-TE_S29_L001_R2_001
        72.0%
        47%
        18.4
        3-4GRA-3-6-Fec-TE_S97_L001_R1_001
        73.8%
        47%
        22.7
        3-4GRA-3-6-Fec-TE_S97_L001_R2_001
        73.3%
        47%
        22.7
        3-4GRA-3-7-Fec-TE_S114_L001_R1_001
        73.9%
        47%
        19.8
        3-4GRA-3-7-Fec-TE_S114_L001_R2_001
        72.5%
        47%
        19.8
        3-4GRA-3-8-Fec-TE_S64_L001_R1_001
        73.7%
        48%
        21.0
        3-4GRA-3-8-Fec-TE_S64_L001_R2_001
        73.2%
        48%
        21.0
        3-4GRA-4-1-Fec-TE_S2_L001_R1_001
        71.5%
        50%
        18.0
        3-4GRA-4-1-Fec-TE_S2_L001_R2_001
        70.5%
        50%
        18.0
        3-4GRA-4-2-Fec-TE_S76_L001_R1_001
        76.1%
        50%
        19.7
        3-4GRA-4-2-Fec-TE_S76_L001_R2_001
        75.6%
        50%
        19.7
        3-4GRA-4-3-Fec-TE_S115_L001_R1_001
        77.6%
        50%
        19.9
        3-4GRA-4-3-Fec-TE_S115_L001_R2_001
        76.6%
        50%
        19.9
        3-4GRA-4-4-Fec-TE_S46_L001_R1_001
        76.3%
        50%
        17.3
        3-4GRA-4-4-Fec-TE_S46_L001_R2_001
        75.5%
        50%
        17.3
        3-4GRA-4-5-Fec-TE_S142_L001_R1_001
        74.7%
        48%
        19.6
        3-4GRA-4-5-Fec-TE_S142_L001_R2_001
        73.7%
        48%
        19.6
        3-4GRA-4-6-Fec-TE_S93_L001_R1_001
        73.7%
        50%
        17.3
        3-4GRA-4-6-Fec-TE_S93_L001_R2_001
        72.6%
        50%
        17.3
        3-4GRA-4-7-Fec-TE_S12_L001_R1_001
        74.6%
        51%
        18.3
        3-4GRA-4-7-Fec-TE_S12_L001_R2_001
        73.5%
        51%
        18.3
        3-4GRA-4-8-Fec-TE_S22_L001_R1_001
        76.4%
        50%
        18.0
        3-4GRA-4-8-Fec-TE_S22_L001_R2_001
        74.9%
        50%
        18.0
        3-4GRA-5-1-Fec-TE_S143_L001_R1_001
        75.0%
        50%
        19.0
        3-4GRA-5-1-Fec-TE_S143_L001_R2_001
        73.9%
        50%
        19.0
        3-4GRA-5-2-Fec-TE_S110_L001_R1_001
        73.1%
        50%
        20.0
        3-4GRA-5-2-Fec-TE_S110_L001_R2_001
        72.3%
        50%
        20.0
        3-4GRA-5-3-Fec-TE_S109_L001_R1_001
        74.5%
        49%
        20.8
        3-4GRA-5-3-Fec-TE_S109_L001_R2_001
        74.2%
        50%
        20.8
        3-4GRA-5-4-Fec-TE_S11_L001_R1_001
        71.2%
        51%
        19.6
        3-4GRA-5-4-Fec-TE_S11_L001_R2_001
        70.6%
        51%
        19.6
        3-4GRA-5-5-Fec-TE_S134_L001_R1_001
        77.4%
        51%
        20.5
        3-4GRA-5-5-Fec-TE_S134_L001_R2_001
        76.6%
        51%
        20.5
        3-4GRA-5-6-Fec-TE_S153_L001_R1_001
        75.6%
        51%
        21.9
        3-4GRA-5-6-Fec-TE_S153_L001_R2_001
        75.4%
        51%
        21.9
        3-4GRA-5-7-Fec-TE_S41_L001_R1_001
        66.4%
        50%
        16.8
        3-4GRA-5-7-Fec-TE_S41_L001_R2_001
        65.9%
        50%
        16.8
        3-4GRA-5-8-Fec-TE_S78_L001_R1_001
        78.7%
        50%
        22.0
        3-4GRA-5-8-Fec-TE_S78_L001_R2_001
        78.6%
        50%
        22.0
        5-6GRA-1-1-Fec-TE_S136_L001_R1_001
        74.9%
        50%
        19.0
        5-6GRA-1-1-Fec-TE_S136_L001_R2_001
        74.3%
        50%
        19.0
        5-6GRA-1-3-Fec-TE_S44_L001_R1_001
        70.1%
        50%
        17.1
        5-6GRA-1-3-Fec-TE_S44_L001_R2_001
        69.5%
        50%
        17.1
        5-6GRA-1-4-Fec-TE_S131_L001_R1_001
        74.2%
        50%
        19.5
        5-6GRA-1-4-Fec-TE_S131_L001_R2_001
        73.8%
        50%
        19.5
        5-6GRA-1-5-Fec-TE_S26_L001_R1_001
        73.5%
        51%
        18.0
        5-6GRA-1-5-Fec-TE_S26_L001_R2_001
        73.3%
        51%
        18.0
        5-6GRA-1-6-Fec-TE_S103_L001_R1_001
        70.4%
        51%
        16.6
        5-6GRA-1-6-Fec-TE_S103_L001_R2_001
        70.3%
        51%
        16.6
        5-6GRA-1-7-Fec-TE_S68_L001_R1_001
        71.3%
        50%
        19.8
        5-6GRA-1-7-Fec-TE_S68_L001_R2_001
        71.2%
        50%
        19.8
        5-6GRA-1-8-Fec-TE_S20_L001_R1_001
        68.5%
        50%
        18.2
        5-6GRA-1-8-Fec-TE_S20_L001_R2_001
        66.7%
        50%
        18.2
        5-6GRA-2-1-Fec-TE_S38_L001_R1_001
        70.4%
        50%
        16.0
        5-6GRA-2-1-Fec-TE_S38_L001_R2_001
        69.6%
        51%
        16.0
        5-6GRA-2-2-Fec-TE_S39_L001_R1_001
        71.5%
        50%
        16.5
        5-6GRA-2-2-Fec-TE_S39_L001_R2_001
        71.5%
        50%
        16.5
        5-6GRA-2-3-Fec-TE_S17_L001_R1_001
        73.8%
        50%
        19.7
        5-6GRA-2-3-Fec-TE_S17_L001_R2_001
        72.8%
        50%
        19.7
        5-6GRA-2-4-Fec-TE_S30_L001_R1_001
        75.1%
        50%
        18.9
        5-6GRA-2-4-Fec-TE_S30_L001_R2_001
        73.7%
        50%
        18.9
        5-6GRA-2-5-Fec-TE_S80_L001_R1_001
        73.9%
        50%
        17.6
        5-6GRA-2-5-Fec-TE_S80_L001_R2_001
        73.2%
        51%
        17.6
        5-6GRA-2-6-Fec-TE_S28_L001_R1_001
        75.4%
        51%
        18.8
        5-6GRA-2-6-Fec-TE_S28_L001_R2_001
        73.0%
        51%
        18.8
        5-6GRA-2-7-Fec-TE_S70_L001_R1_001
        72.6%
        50%
        15.6
        5-6GRA-2-7-Fec-TE_S70_L001_R2_001
        71.7%
        50%
        15.6
        5-6GRA-2-8-Fec-TE_S14_L001_R1_001
        71.6%
        50%
        15.1
        5-6GRA-2-8-Fec-TE_S14_L001_R2_001
        70.6%
        50%
        15.1
        5-6GRA-3-1-Fec-TE_S51_L001_R1_001
        73.5%
        47%
        20.1
        5-6GRA-3-1-Fec-TE_S51_L001_R2_001
        72.8%
        47%
        20.1
        5-6GRA-3-2-Fec-TE_S77_L001_R1_001
        77.0%
        47%
        21.1
        5-6GRA-3-2-Fec-TE_S77_L001_R2_001
        76.4%
        47%
        21.1
        5-6GRA-3-3-Fec-TE_S4_L001_R1_001
        70.8%
        47%
        18.0
        5-6GRA-3-3-Fec-TE_S4_L001_R2_001
        69.8%
        47%
        18.0
        5-6GRA-3-4-Fec-TE_S144_L001_R1_001
        74.6%
        48%
        19.3
        5-6GRA-3-4-Fec-TE_S144_L001_R2_001
        74.0%
        48%
        19.3
        5-6GRA-3-5-Fec-TE_S123_L001_R1_001
        71.5%
        47%
        19.2
        5-6GRA-3-5-Fec-TE_S123_L001_R2_001
        70.8%
        48%
        19.2
        5-6GRA-3-6-Fec-TE_S82_L001_R1_001
        75.2%
        47%
        22.8
        5-6GRA-3-6-Fec-TE_S82_L001_R2_001
        74.2%
        48%
        22.8
        5-6GRA-3-7-Fec-TE_S130_L001_R1_001
        78.7%
        47%
        22.4
        5-6GRA-3-7-Fec-TE_S130_L001_R2_001
        78.4%
        47%
        22.4
        5-6GRA-3-8-Fec-TE_S124_L001_R1_001
        69.4%
        47%
        19.1
        5-6GRA-3-8-Fec-TE_S124_L001_R2_001
        68.0%
        48%
        19.1
        5-6GRA-3-8Vag-TE_S163_L001_R1_001
        97.5%
        47%
        19.0
        5-6GRA-3-8Vag-TE_S163_L001_R2_001
        96.6%
        47%
        19.0
        5-6GRA-4-1-Fec-TE_S52_L001_R1_001
        76.7%
        50%
        19.8
        5-6GRA-4-1-Fec-TE_S52_L001_R2_001
        75.8%
        51%
        19.8
        5-6GRA-4-2-Fec-TE_S45_L001_R1_001
        66.0%
        51%
        14.7
        5-6GRA-4-2-Fec-TE_S45_L001_R2_001
        65.3%
        52%
        14.7
        5-6GRA-4-3-Fec-TE_S48_L001_R1_001
        77.4%
        50%
        23.4
        5-6GRA-4-3-Fec-TE_S48_L001_R2_001
        76.2%
        50%
        23.4
        5-6GRA-4-4-Fec-TE_S104_L001_R1_001
        76.4%
        51%
        22.2
        5-6GRA-4-4-Fec-TE_S104_L001_R2_001
        75.7%
        51%
        22.2
        5-6GRA-4-5-Fec-TE_S118_L001_R1_001
        73.4%
        48%
        21.6
        5-6GRA-4-5-Fec-TE_S118_L001_R2_001
        72.4%
        49%
        21.6
        5-6GRA-4-6-Fec-TE_S135_L001_R1_001
        79.1%
        51%
        22.2
        5-6GRA-4-6-Fec-TE_S135_L001_R2_001
        77.5%
        51%
        22.2
        5-6GRA-4-7-Fec-TE_S151_L001_R1_001
        75.8%
        50%
        21.0
        5-6GRA-4-7-Fec-TE_S151_L001_R2_001
        75.1%
        50%
        21.0
        5-6GRA-4-8-Fec-TE_S9_L001_R1_001
        80.3%
        51%
        24.4
        5-6GRA-4-8-Fec-TE_S9_L001_R2_001
        78.9%
        51%
        24.4
        5-6GRA-5-1-Fec-TE_S111_L001_R1_001
        74.6%
        50%
        20.6
        5-6GRA-5-1-Fec-TE_S111_L001_R2_001
        74.2%
        50%
        20.6
        5-6GRA-5-2-Fec-TE_S55_L001_R1_001
        77.7%
        50%
        22.2
        5-6GRA-5-2-Fec-TE_S55_L001_R2_001
        76.9%
        50%
        22.2
        5-6GRA-5-3-Fec-TE_S79_L001_R1_001
        86.2%
        50%
        23.7
        5-6GRA-5-3-Fec-TE_S79_L001_R2_001
        85.4%
        50%
        23.7
        5-6GRA-5-4-Fec-TE_S141_L001_R1_001
        71.1%
        50%
        19.4
        5-6GRA-5-4-Fec-TE_S141_L001_R2_001
        70.6%
        50%
        19.4
        5-6GRA-5-5-Fec-TE_S155_L001_R1_001
        39.6%
        48%
        27.4
        5-6GRA-5-5-Fec-TE_S155_L001_R2_001
        39.5%
        48%
        27.4
        5-6GRA-5-6-Fec-TE_S25_L001_R1_001
        76.4%
        51%
        23.5
        5-6GRA-5-6-Fec-TE_S25_L001_R2_001
        75.0%
        51%
        23.5
        5-6GRA-5-7-Fec-TE_S148_L001_R1_001
        75.7%
        50%
        19.5
        5-6GRA-5-7-Fec-TE_S148_L001_R2_001
        75.2%
        50%
        19.5
        5-6GRA-5-8-Fec-TE_S75_L001_R1_001
        76.9%
        50%
        18.4
        5-6GRA-5-8-Fec-TE_S75_L001_R2_001
        76.1%
        50%
        18.4
        7-8GRA-1-1-Fec-TE_S132_L001_R1_001
        74.7%
        50%
        18.9
        7-8GRA-1-1-Fec-TE_S132_L001_R2_001
        73.5%
        50%
        18.9
        7-8GRA-1-3-Fec-TE_S35_L001_R1_001
        68.7%
        51%
        14.8
        7-8GRA-1-3-Fec-TE_S35_L001_R2_001
        68.2%
        51%
        14.8
        7-8GRA-1-4-Fec-TE_S60_L001_R1_001
        73.8%
        51%
        19.6
        7-8GRA-1-4-Fec-TE_S60_L001_R2_001
        73.1%
        51%
        19.6
        7-8GRA-1-5-Fec-TE_S139_L001_R1_001
        71.2%
        51%
        22.2
        7-8GRA-1-5-Fec-TE_S139_L001_R2_001
        70.5%
        51%
        22.2
        7-8GRA-1-6-Fec-TE_S106_L001_R1_001
        78.1%
        51%
        21.5
        7-8GRA-1-6-Fec-TE_S106_L001_R2_001
        77.3%
        51%
        21.5
        7-8GRA-1-7-Fec-TE_S99_L001_R1_001
        73.9%
        50%
        17.3
        7-8GRA-1-7-Fec-TE_S99_L001_R2_001
        71.9%
        50%
        17.3
        7-8GRA-1-8-Fec-TE_S108_L001_R1_001
        72.6%
        50%
        20.5
        7-8GRA-1-8-Fec-TE_S108_L001_R2_001
        71.8%
        50%
        20.5
        7-8GRA-2-1-Fec-TE_S6_L001_R1_001
        72.0%
        50%
        16.7
        7-8GRA-2-1-Fec-TE_S6_L001_R2_001
        70.5%
        50%
        16.7
        7-8GRA-2-2-Fec-TE_S37_L001_R1_001
        72.4%
        49%
        19.3
        7-8GRA-2-2-Fec-TE_S37_L001_R2_001
        72.3%
        49%
        19.3
        7-8GRA-2-3-Fec-TE_S121_L001_R1_001
        68.1%
        50%
        17.3
        7-8GRA-2-3-Fec-TE_S121_L001_R2_001
        65.9%
        50%
        17.3
        7-8GRA-2-4-Fec-TE_S40_L001_R1_001
        69.0%
        50%
        19.5
        7-8GRA-2-4-Fec-TE_S40_L001_R2_001
        68.1%
        50%
        19.5
        7-8GRA-2-4Nas-TE_S158_L001_R1_001
        92.7%
        54%
        23.2
        7-8GRA-2-4Nas-TE_S158_L001_R2_001
        92.0%
        54%
        23.2
        7-8GRA-2-5-Fec-TE_S42_L001_R1_001
        77.4%
        51%
        21.1
        7-8GRA-2-5-Fec-TE_S42_L001_R2_001
        76.6%
        51%
        21.1
        7-8GRA-2-6-Fec-TE_S61_L001_R1_001
        74.4%
        50%
        17.5
        7-8GRA-2-6-Fec-TE_S61_L001_R2_001
        73.4%
        50%
        17.5
        7-8GRA-2-7-Fec-TE_S81_L001_R1_001
        73.2%
        49%
        19.2
        7-8GRA-2-7-Fec-TE_S81_L001_R2_001
        72.7%
        49%
        19.2
        7-8GRA-2-8-Fec-TE_S67_L001_R1_001
        73.8%
        50%
        17.5
        7-8GRA-2-8-Fec-TE_S67_L001_R2_001
        73.0%
        50%
        17.5
        7-8GRA-3-1-Fec-TE_S112_L001_R1_001
        74.4%
        48%
        21.8
        7-8GRA-3-1-Fec-TE_S112_L001_R2_001
        73.5%
        48%
        21.8
        7-8GRA-3-2-Fec-TE_S154_L001_R1_001
        75.8%
        47%
        21.9
        7-8GRA-3-2-Fec-TE_S154_L001_R2_001
        74.7%
        48%
        21.9
        7-8GRA-3-3-Fec-TE_S83_L001_R1_001
        72.1%
        48%
        21.1
        7-8GRA-3-3-Fec-TE_S83_L001_R2_001
        71.3%
        48%
        21.1
        7-8GRA-3-3Nas-TE_S159_L001_R1_001
        95.9%
        54%
        25.1
        7-8GRA-3-3Nas-TE_S159_L001_R2_001
        95.0%
        54%
        25.1
        7-8GRA-3-4-Fec-TE_S24_L001_R1_001
        71.2%
        48%
        17.9
        7-8GRA-3-4-Fec-TE_S24_L001_R2_001
        70.2%
        48%
        17.9
        7-8GRA-3-5-Fec-TE_S91_L001_R1_001
        70.7%
        47%
        20.4
        7-8GRA-3-5-Fec-TE_S91_L001_R2_001
        70.3%
        47%
        20.4
        7-8GRA-3-6-Fec-TE_S21_L001_R1_001
        75.0%
        48%
        21.3
        7-8GRA-3-6-Fec-TE_S21_L001_R2_001
        74.0%
        48%
        21.3
        7-8GRA-3-7-Fec-TE_S56_L001_R1_001
        71.0%
        48%
        19.6
        7-8GRA-3-7-Fec-TE_S56_L001_R2_001
        70.6%
        48%
        19.6
        7-8GRA-3-8-Fec-TE_S19_L001_R1_001
        75.9%
        48%
        24.8
        7-8GRA-3-8-Fec-TE_S19_L001_R2_001
        75.2%
        48%
        24.8
        7-8GRA-4-1-Fec-TE_S120_L001_R1_001
        71.2%
        50%
        20.6
        7-8GRA-4-1-Fec-TE_S120_L001_R2_001
        70.3%
        50%
        20.6
        7-8GRA-4-2-Fec-TE_S137_L001_R1_001
        73.3%
        50%
        20.4
        7-8GRA-4-2-Fec-TE_S137_L001_R2_001
        72.3%
        50%
        20.4
        7-8GRA-4-3-Fec-TE_S102_L001_R1_001
        71.1%
        50%
        16.1
        7-8GRA-4-3-Fec-TE_S102_L001_R2_001
        70.6%
        50%
        16.1
        7-8GRA-4-4-Fec-TE_S7_L001_R1_001
        71.9%
        50%
        17.3
        7-8GRA-4-4-Fec-TE_S7_L001_R2_001
        71.0%
        50%
        17.3
        7-8GRA-4-5-Fec-TE_S43_L001_R1_001
        71.8%
        49%
        16.7
        7-8GRA-4-5-Fec-TE_S43_L001_R2_001
        71.3%
        49%
        16.7
        7-8GRA-4-6-Fec-TE_S86_L001_R1_001
        69.6%
        51%
        15.2
        7-8GRA-4-6-Fec-TE_S86_L001_R2_001
        68.7%
        51%
        15.2
        7-8GRA-4-7-Fec-TE_S74_L001_R1_001
        75.5%
        50%
        17.8
        7-8GRA-4-7-Fec-TE_S74_L001_R2_001
        74.5%
        50%
        17.8
        7-8GRA-4-8-Fec-TE_S90_L001_R1_001
        71.8%
        50%
        18.5
        7-8GRA-4-8-Fec-TE_S90_L001_R2_001
        70.9%
        51%
        18.5
        7-8GRA-5-1-Fec-TE_S127_L001_R1_001
        73.3%
        50%
        21.8
        7-8GRA-5-1-Fec-TE_S127_L001_R2_001
        72.5%
        50%
        21.8
        7-8GRA-5-2-Fec-TE_S126_L001_R1_001
        71.2%
        49%
        20.2
        7-8GRA-5-2-Fec-TE_S126_L001_R2_001
        70.6%
        50%
        20.2
        7-8GRA-5-3-Fec-TE_S94_L001_R1_001
        71.1%
        50%
        16.9
        7-8GRA-5-3-Fec-TE_S94_L001_R2_001
        70.6%
        50%
        16.9
        7-8GRA-5-4-Fec-TE_S100_L001_R1_001
        73.1%
        50%
        16.3
        7-8GRA-5-4-Fec-TE_S100_L001_R2_001
        72.4%
        50%
        16.3
        7-8GRA-5-5-Fec-TE_S96_L001_R1_001
        74.5%
        51%
        23.1
        7-8GRA-5-5-Fec-TE_S96_L001_R2_001
        74.0%
        51%
        23.1
        7-8GRA-5-6-Fec-TE_S128_L001_R1_001
        75.7%
        50%
        19.0
        7-8GRA-5-6-Fec-TE_S128_L001_R2_001
        74.5%
        51%
        19.0
        7-8GRA-5-6Nas-TE_S157_L001_R1_001
        96.3%
        53%
        26.4
        7-8GRA-5-6Nas-TE_S157_L001_R2_001
        95.1%
        53%
        26.4
        7-8GRA-5-7-Fec-TE_S36_L001_R1_001
        66.0%
        51%
        13.7
        7-8GRA-5-7-Fec-TE_S36_L001_R2_001
        65.5%
        51%
        13.7
        7-8GRA-5-8-Fec-TE_S119_L001_R1_001
        72.3%
        50%
        22.2
        7-8GRA-5-8-Fec-TE_S119_L001_R2_001
        71.8%
        50%
        22.2
        7-8GRA-5-8Vag-TE_S161_L001_R1_001
        97.3%
        51%
        16.0
        7-8GRA-5-8Vag-TE_S161_L001_R2_001
        96.5%
        51%
        16.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
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        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

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        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        328 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.15 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.